Although railway networks are the one of the best in the world, there are many flight routes in Japan. The most busiest route in Japan, may be the busiest in the world is Tokyo/Haneda - Sapporo/Shin-Chitose which 4 Japanese airlines are flying hourly by large Boeing aircraft, such as B777. Second busiest is Tokyo/Haneda - Fukuoka.
These two cities are more than 4 hours by train and therefore airplane dominates the routes but on the other hand, if the distance is shorter than 3 hours, train dominates. Therefore there are plenty of cities which are not connected with Tokyo by air routes or abolished when Shinkansen was commenced.
Japanese domestic flights are little bit different from international flights. At first, you do not have to show your ID upon boarding. Then, beverage on board is totally different. There is a soup but no cola. Apple juice is available but orange juice is not.